Contacts of the strand formed by residues 47 - 55 (chain K) in PDB entry 4M75
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 47 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4J PRO* 4.1 4.2 - - - +
26K VAL* 3.9 22.2 - - + -
38K LEU* 3.5 22.2 - - + -
40K SER 3.8 2.2 - - - -
41K ILE* 3.5 15.7 - - + -
45K MSE 2.9 19.7 - - - +
46K ASN* 1.3 75.0 - - - +
48K ALA* 1.3 61.1 + - - +
49K LEU* 3.9 10.3 + - + -
71K VAL 3.6 3.5 - - - +
72K PHE* 3.6 2.3 - - - -
73K LEU* 2.9 46.8 + - + +
78K VAL* 4.6 11.0 - - + -
81K ILE* 3.6 14.8 - - + -
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Residues in contact with ALA 48 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4J PRO* 3.5 8.8 - - + +
7J LEU* 2.8 36.3 - - + -
38K LEU* 2.6 31.2 - - - +
39K GLU* 3.5 8.8 + - + -
40K SER* 2.9 31.9 + - - +
47K VAL* 1.3 73.0 - - - +
49K LEU* 1.3 58.1 + - - +
71K VAL 3.5 4.7 - - - -
72K PHE* 4.9 0.4 - - - +
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Residues in contact with LEU 49 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24K VAL* 3.8 11.7 - - + +
26K VAL* 4.4 10.1 - - + -
34K TYR* 3.8 19.3 - - + +
36K GLY* 3.6 25.6 - - - +
37K ARG 3.4 14.6 - - - +
38K LEU* 3.6 21.8 - - + -
39K GLU* 4.7 1.3 - - - +
47K VAL* 3.9 12.3 - - + +
48K ALA* 1.3 84.7 - - - +
50K SER* 1.3 63.6 + - - +
52K ALA* 4.1 11.9 - - + -
70K ASP* 3.2 9.4 - - - +
71K VAL* 2.9 47.6 + - + +
73K LEU* 5.1 5.4 - - + -
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Residues in contact with SER 50 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36K GLY* 3.9 0.2 - - - -
37K ARG* 2.8 36.1 + - - +
39K GLU* 3.6 24.9 + - - +
49K LEU* 1.3 74.9 + - - +
51K SER* 1.3 79.2 + - - +
52K ALA 3.4 0.7 - - - -
70K ASP* 3.8 14.8 + - - +
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Residues in contact with SER 51 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35K SER 3.6 5.9 - - - +
36K GLY* 4.1 1.0 - - - -
37K ARG* 4.7 3.6 + - - +
50K SER* 1.3 85.8 + - - +
52K ALA* 1.3 65.5 + - - +
53K THR* 4.6 4.2 - - - +
67K PHE 4.1 10.1 - - - -
68K ASN 4.0 18.5 + - - -
69K SER 3.7 12.8 + - - -
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Residues in contact with ALA 52 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34K TYR* 4.8 10.5 - - + -
35K SER 3.0 12.8 - - - +
36K GLY* 4.2 0.9 - - - -
49K LEU* 4.1 15.7 - - + -
50K SER 3.4 0.6 - - - -
51K SER* 1.3 79.7 - - - +
53K THR* 1.3 55.3 + - - +
67K PHE* 2.5 46.7 + - + +
69K SER 4.7 0.8 + - - -
71K VAL* 3.7 28.9 - - + +
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Residues in contact with THR 53 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33K LEU 3.5 1.2 - - - +
34K TYR* 3.2 6.3 - - - -
35K SER* 2.9 41.8 + - - -
51K SER 4.6 4.7 - - - +
52K ALA* 1.3 76.7 - - - +
54K GLU* 1.3 58.8 + - - +
55K HIS* 3.9 20.0 + - - -
64K LEU* 5.1 0.9 - - + -
66K LYS* 2.3 39.7 - - + +
67K PHE* 4.9 1.8 - - - +
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Residues in contact with GLU 54 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160H HIS 4.7 1.6 - - - +
161H GLY* 3.8 14.2 - - - +
19J LYS* 2.4 24.7 + - - +
32K LEU* 3.7 14.4 - - + +
33K LEU 3.2 4.0 - - - +
34K TYR* 2.1 55.2 + - + +
53K THR* 1.3 70.9 - - - +
55K HIS* 1.3 80.7 + - - +
63K LEU 4.0 0.2 - - - +
64K LEU* 3.3 0.9 - - - -
65K ASN* 2.5 47.7 + - + +
67K PHE* 4.7 7.5 - - + -
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Residues in contact with HIS 55 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32K LEU* 4.5 5.8 - - - -
33K LEU* 2.4 57.5 + - + +
35K SER* 6.1 3.4 - - - -
53K THR* 3.9 18.1 + - - -
54K GLU* 1.3 88.0 - - - +
56K TYR* 1.3 55.8 + - - +
57K GLU* 3.7 19.2 - - + +
62K LYS* 3.1 20.0 + - - +
63K LEU 3.1 10.3 - - - +
64K LEU* 2.4 46.8 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il